Contacts of the strand formed by residues 1159 - 1164 (chain D) in PDB entry 6X34
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR1159 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1153D ILE* 3.8 0.7 - - - +
1154D ASP* 3.0 31.8 + - - +
1157D GLU* 4.1 15.0 - - - -
1158D ASN* 1.3 78.5 - - - +
1160D ILE* 1.3 65.8 + - - +
1161D ILE* 4.3 14.2 - - - +
1177D THR* 3.6 25.1 - - - -
1179D PHE 4.3 2.2 - - - -
1182D ILE* 3.9 0.6 - - - +
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Residues in contact with ILE1160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104D TRP* 4.0 23.6 - - + +
1122D TYR* 3.6 37.9 - - + -
1152D MET 4.0 3.4 - - - +
1153D ILE* 3.7 24.7 - - + +
1159D THR* 1.3 79.5 - - - +
1161D ILE* 1.3 67.8 + - - +
1162D PHE* 3.6 33.2 - - + -
1176D GLU 4.3 0.5 - - - +
1177D THR* 4.0 4.8 + - - -
1178D ALA* 3.1 31.6 + - + +
1179D PHE* 4.2 15.4 + - + +
1182D ILE* 4.0 9.2 - - + -
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Residues in contact with ILE1161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1151D CYS* 3.9 0.3 - - - -
1152D MET* 2.9 48.0 + - + +
1154D ASP* 5.0 9.6 - - + -
1159D THR* 4.3 16.2 - - - +
1160D ILE* 1.3 85.7 - - - +
1162D PHE* 1.3 72.9 + - - +
1163D THR* 4.0 5.7 + - - +
1168D VAL* 4.8 21.3 - - + -
1176D GLU* 4.1 17.5 - - + +
1177D THR* 5.8 0.2 - - - -
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Residues in contact with PHE1162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102D VAL* 4.6 0.7 - - + -
1103D GLY* 3.8 25.8 - - - -
1104D TRP 5.1 0.7 - - - -
1122D TYR* 5.9 3.8 - - + -
1123D VAL* 4.9 6.7 - - - -
1124D PHE* 3.8 44.2 - + + -
1131D ARG* 6.0 3.1 - - + -
1150D GLY 3.6 2.9 - - - +
1151D CYS* 3.6 23.1 - - + -
1160D ILE* 3.6 24.0 + - + -
1161D ILE* 1.3 82.2 - - - +
1163D THR* 1.3 61.0 + - - +
1164D LEU* 4.1 15.0 - - + -
1167D GLU 4.3 0.2 - - - +
1168D VAL* 4.5 1.0 - - - -
1169D LEU* 3.8 26.8 + - + +
1178D ALA* 3.6 31.2 - - + -
1179D PHE* 6.4 0.2 - - + -
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Residues in contact with THR1163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089D TYR* 4.3 19.7 - - + +
1149D VAL* 3.4 2.9 - - - +
1150D GLY* 2.5 55.2 + - - +
1151D CYS* 4.5 1.2 + - - -
1152D MET* 5.0 3.5 + - - +
1161D ILE* 4.4 9.7 + - - +
1162D PHE* 1.3 72.8 - - - +
1164D LEU* 1.3 65.2 + - - +
1165D ASN 4.0 0.6 + - - -
1166D GLY* 3.7 14.1 - - - +
1167D GLU 3.7 25.4 - - - +
1168D VAL* 5.3 2.5 - - + +
1213D PHE 5.5 2.5 - - - +
1216D ILE* 5.9 2.0 - - + -
1217D CYS* 6.0 4.4 - - + +
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Residues in contact with LEU1164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124D PHE* 4.0 22.2 - - + -
1140D GLY* 5.8 3.6 - - - -
1141D ARG 5.3 5.2 - - - +
1142D PRO 5.7 0.9 - - - +
1143D TRP* 3.4 35.0 - - + +
1147D ASP* 6.4 1.3 - - + -
1149D VAL* 4.2 14.8 - - + +
1150D GLY 5.2 0.2 - - - +
1162D PHE* 4.2 12.3 - - + -
1163D THR* 1.3 77.7 - - - +
1165D ASN* 1.3 80.2 + - - +
1167D GLU* 2.9 28.8 + - - +
1169D LEU* 4.1 25.1 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il